FIMO Results

FIMO - Motif search tool

FIMO version 5.5.5, (Release date: Thu Sep 14 08:48:04 2023 +1000)

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/fimo-output-format.html.
To get a copy of the FIMO software please access https://meme-suite.org

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

DATABASE AND MOTIFS

  DATABASE MOA24_gain_diff.fa
  
  Database contains 1289 sequences, 33082 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-YCTSCTG
        7
        CCTGCTG
       
        2-CWGCCA
        6
        CAGCCA
       
        3-MTGASTCAK
        9
        ATGAGTCAT
       
        4-CTGGCCA
        7
        CTGGCCA
       
        5-CCCCCTWGMG
        10
        CCCCCTTGAG
       
Random model letter frequencies (./background):

A 0.262 C 0.238 G 0.238 T 0.262

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-YCTSCTG	7	CCTGCTG
2-CWGCCA	6	CAGCCA
3-MTGASTCAK	9	ATGAGTCAT
4-CTGGCCA	7	CTGGCCA
5-CCCCCTWGMG	10	CCCCCTTGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 20 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the TSV (tab-delimited values) output file fimo.tsv, the GFF3 file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
The table is sorted by increasing p-value.

Motif ID	Alt ID	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
4-CTGGCCA	STREME-4	chr16	-	3131963	3131969	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr19	+	3459108	3459114	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr19	-	3459109	3459115	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr6	+	27866500	27866506	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr2	-	43524457	43524463	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr18	+	45785431	45785437	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr18	-	45785432	45785438	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr18	+	62586358	62586364	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr18	-	62586359	62586365	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr16	-	65118171	65118177	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr15	+	78241119	78241125	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr15	-	78241120	78241126	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr9	+	96137445	96137451	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr9	-	96137446	96137452	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr5	+	96175318	96175324	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr3	+	99173205	99173211	5.26e-05	0.132	ctggcca
4-CTGGCCA	STREME-4	chr7	-	105657108	105657114	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr3	-	123719303	123719309	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr3	+	170695819	170695825	5.26e-05	0.132	CTGGCCA
4-CTGGCCA	STREME-4	chr2	-	173415099	173415105	5.26e-05	0.132	CTGGCCA

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_6 --bgfile ./background --motif 4-CTGGCCA streme_out/streme.xml MOA24_gain_diff.fa

Settings:


  
    output_directory = fimo_out_6
    MEME file name = streme_out/streme.xml
    sequence file name = MOA24_gain_diff.fa
  
  
    background file name = ./background
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = true
  
  
    text only = false
    scan both strands = true
    max strand = false
  
  
    threshold type = p-value
    output theshold = 0.0001
    pseudocount = 0.1
  
  
    alpha = 1
    verbosity = 1

This information can be useful in the event you wish to report a problem with the FIMO software.

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output_directory = fimo_out_6	MEME file name = streme_out/streme.xml	sequence file name = MOA24_gain_diff.fa
background file name = ./background	alphabet = DNA	max stored scores = 100000
allow clobber = true	compute q-values = true	parse genomic coord. = true
text only = false	scan both strands = true	max strand = false
threshold type = p-value	output theshold = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1